library(fmsb)
library(dplyr)
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
library(ggplot2)
Gibran Hemani and Nic Timpson
January 26, 2023
Sample of individuals who have had heart surgery, followed up and some number go on to have kidney disease. What is the predictive rsq of a metabolite on kidney disease outcome, that has 80% power to be detected after multiple testing correction?
Call libraries
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Define model
sim <- function(ncase, ncontrol, b)
{
met <- rnorm(ncase+ncontrol)
y <- rbinom(ncase+ncontrol, 1, plogis(log(ncase/(ncase+ncontrol)) + met*b + rnorm(ncase+ncontrol)))
table(y)
mod <- glm(y ~ met)
rsq <- NagelkerkeR2(mod)$R2
pval <- summary(mod)$coef[2,4]
return(tibble(rsq, pval, ncase, ncontrol, b))
}
Set parameters
Run
Visualise